Susan Murphy (Reese Witherspoon) is hit by a meteor on the day of her wedding to weatherman Derek Dietl (Paul Rudd), absorbing a substance called quantonium and growing into a giantess. Alerted to the meteor crash, the military arrive and capture Susan. She is labeled a monster, renamed "Ginormica" by the government, and sent to a top-secret prison facility headed by General W.R. Monger (Kiefer Sutherland) and containing other monsters: B.O.B. (Seth Rogen), a brainless, indestructible gelatinous blob; Dr. Cockroach, Ph.D. (Hugh Laurie), a mad scientist with the head and abilities of a cockroach; the Missing Link (Will Arnett), an amphibious fish-ape hybrid; and Insectosaurus, a colossal grub that is even larger than Susan. The monsters are forbidden to have any contact with the outside world; while the other monsters have been living contentedly with this lifestyle for the past 50 years, Susan feels incredibly isolated and wishes to return to her old life.

An alien named Gallaxhar (Rainn Wilson) detects the quantonium radiation emanating from Earth and deploys a gigantic robotic probe to find it and extract it from its source, Susan. After a botched attempt by the President of the United States (Stephen Colbert) to make first contact with the robot, it begins destroying everything in sight, resisting all conventional military force used against it. General Monger convinces the President to use the monsters to fight the robot instead. The monsters accept the mission with the promise of freedom if they succeed. Arriving in San Francisco, Susan is chased by the robot across the city to the Golden Gate Bridge, where the monsters are able to defeat the robot.